Welcome to chewBBACA’s documentation!

Getting Started

• Overview
• Important Notes
• Useful links
• Installation
• Quick Start

User Guide

• CreateSchema - Create a gene-by-gene schema
• AlleleCall - Determine the allelic profiles of a set of genomes
• SchemaEvaluator - Build an interactive report for schema evaluation
• AlleleCallEvaluator - Build an interactive report for allele calling results evaluation
• ExtractCgMLST - Determine the set of loci that constitute the core genome
• RemoveGenes - Remove a set of loci from allele calling results
• PrepExternalSchema - Adapt an external schema to be used with chewBBACA
• JoinProfiles - Join allele calling results from different runs
• UniprotFinder - Retrieve annotations for loci in a schema
• DownloadSchema - Download a schema from Chewie-NS
• LoadSchema - Upload a schema to Chewie-NS
• SyncSchema - Synchronize a schema with its remote version in Chewie-NS
• NSStats - Retrieve basic information about the species and schemas in Chewie-NS

Tutorials

• Step-by-step Tutorial
• Integration with Chewie-NS

Help and support

• Contacts
• FAQ